Primary intraosseous squamous cell carcinoma (PIOSCC) is a rare central jaw carcinoma derived from odontogenic epithelial remnants. When the tumour arises in an existing cyst, it may be difficult to recognise early PIOSCC and carry out necessary treatment. We report a case diagnosed in a 50-year-old man where timely intervention was delayed and prognosis was affected and the case diagnosed eventually by comprehensive clinical, radiological and histopathological examination.